Module 1, Lecture 1: Bioinformatics

author: M Hallett date: January 2016 autosize:true font-family: ‘Helvetica’ #output: beamer-presentation #title: “Sample Document” #output: pdf_document

COMP-364 Tools for the Life Sciences

Logistics

www.bci.mcgill.ca My lab website
www.bci.mcgill.ca/home/?page_id=811 Course Website

MTR 10:35am-11:25am
ENGTR – Trottier Building 2120
Jan 7th 2016 – April 15th 2016

\({\tt michael.t.hallett@mcgill.ca}\)
Office: McIntyre 903
Office Hours: TBA

Mohamed Ghadie, Teaching Assistant
\({\tt mohamed.ghadie@mail.mcgill.ca}\)
Office: TBA
Office Hours: TBA

Course Evaluation & Schedule

Exercise Due Date % of Grade
Assignment 0 Monday, January 25, 2016 10%
Assignment 1 Monday February 8, 2016 10%
Assignment 2 Monday, February 22, 2016 10%
Midterm Week of March 7-11, 2016 20%
Assignment 3 Monday, March 21, 2016 10%
Assignment 4 Monday, April 11, 2016 10%
Final Exam TBA 30%

Infrastucture & General Notes

Infrastucture & General Notes (2)

Infrastucture & General Notes (3)

Some advice

What is Bioinformatics?

Seque: The Importance of Being a Bioinformatician

Seque (2): And the Geeks shall inherit the earth

Seque (3): And the Geeks shall inherit the earth

PubMed.home

Seque (4): And the Geeks shall inherit the earth

PubMed.search

Nice Tool: PubMed Automated Searches

Seque (5): And the Geeks shall inherit the earth

Seque (6): And the Geeks shall inherit the earth

Seque (7): And the Geeks shall inherit the earth

Seque (8): And the Geeks shall inherit the earth

Oncomine

What is Bioinformatics? (2)

What is Bioinformatics? (3)

The Human Genome Project

HGP

The Human Genome Project

HGP

The Human Genome Project

HGP

Then the 1,000 and 10,000 Genome Projects…

1KGenomes

10KGenomes

Catalogues of “functional genomic” information

HapMap SNP

The HapMap project that catalogs single nucleotide polymorphisms and other mutations in human populations.

Catalogues of “functional genomic” information

Yeast-Ste20

Gene Expression Omnibus and other efforts seek to catalogue transcriptional (mRNA expression levels)

Catalogues of “post-genomic” information

Epigenome

The Epigenome project that is attempting to catalogue all epigenetic modifications (e.g. methylation) in different types of human cells (e.g neuronal versus epithelial vs fibroblasts vs endothelial etc.).

Catalogues of “post-genomic” information

PPI

Networks that capture which pairs of proteins interact within a cell or organism. Here this is a bacteria (Treponema palladium). Nodes are proteins and edges (lines) connect two proteins that have been determined to interact. Interactions can be between proteins within a complex (e.g. proteins that comprise the ribosome), proteins that phosphorylate other proteins within signalling cascasdes, protein chaperones that help other proteins fold, or …

Catalogues versus Models

Catalogues versus Models

Can we build a model that accurately predicts how a biological system will behave?

Consider, the Double Helix Model of DNA

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dna.helix.2

Historically,biological models are simple and deterministic


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dna.helix.1

Consider, the Genetic Code

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genetic.code.1


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genetic.code.2

There appear to be very few such simple examples

TF model

Models of Transcription Factor Binding (2)

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TF model


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TF model

Models of Transcription Factor Binding (3)

TF model

Or Models of RNA Binding Proteins

RNA model

The Stochastic Nature of Biological Systems

The list goes on and on: * the genomic organization of a gene, * alternative splicing, * almost every biological process or response (reponse to stress, starvation, heat shock, cold shock, hypoxia, …), * protein translation, * degradation, * protein trafficking, * \(\ldots\)

Probabilistic Models

Markov.chain

Hidden Markov Models

HMM

COMP-364 (c) M Hallett, BCI-McGill

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